kickstart rdock-utils package (#57)

* kickstart rdock-utils package

.github/workflows/build_generic.yml

@@ -33,7 +33,7 @@ jobs:
 
     - name: Build rDock
       run: docker run --rm -v $PWD:/rdock -w /rdock rdock-${{ inputs.distribution }}:base make CXX=${{ inputs.compiler }} -j 2
-    
+
     - name: Test rDock
       run: docker run --rm -v $PWD:/rdock -w /rdock rdock-${{ inputs.distribution }}:base make CXX=${{ inputs.compiler }} test
 

.github/workflows/rdock-utils.yaml

@@ -0,0 +1,50 @@
+name: "[rdock-utils] Lint and Test"
+
+on:
+  pull_request:
+    branches:
+      - main
+
+  push:
+    branches:
+      - main
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v2
+
+    - name: Login to GitHub Container Registry
+      uses: docker/login-action@v2
+      with:
+        registry: ghcr.io
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: Build rdock-utils dev image
+      uses: docker/build-push-action@v5
+      with:
+        context: ./rdock-utils
+        tags: ghcr.io/cbdd/rdock-utils:dev
+        file: ./rdock-utils/Dockerfile
+        target: development
+        cache-from: type=gha,scope=rdock-utils
+        cache-to: type=gha,mode=max,scope=rdock-utils
+        load: true
+
+    - name: flake8
+      run: docker run --rm -v $PWD/rdock-utils:/rdock-utils -w /rdock-utils ghcr.io/cbdd/rdock-utils:dev flake8 .
+
+    - name: black
+      run: docker run --rm -v $PWD/rdock-utils:/rdock-utils -w /rdock-utils ghcr.io/cbdd/rdock-utils:dev black --check .
+
+    - name: isort
+      run: docker run --rm -v $PWD/rdock-utils:/rdock-utils -w /rdock-utils ghcr.io/cbdd/rdock-utils:dev isort --check .
+
+    - name: mypy
+      run: docker run --rm -v $PWD/rdock-utils:/rdock-utils -w /rdock-utils ghcr.io/cbdd/rdock-utils:dev mypy .

rdock-utils/.devcontainer/devcontainer.json

@@ -0,0 +1,47 @@
+{
+	"name": "rdock-utils",
+	"build": {
+		"dockerfile": "../Dockerfile",
+		"context": "..",
+		"target": "development"
+	},
+	"customizations": {
+		"vscode": {
+			"settings": {
+				"python.languageServer": "Pylance",
+				"python.linting.enabled": true,
+				"python.linting.flake8Enabled": true,
+				"python.formatting.provider": "black",
+				"python.linting.mypyEnabled": false,
+				"isort.check": true,
+				"python.testing.pytestEnabled": true,
+				"python.testing.pytestArgs": [
+					"tests"
+				],
+				"python.formatting.blackArgs": [
+					"--line-length",
+					"119"
+				],
+				"isort.args": [
+					"--profile",
+					"black"
+				],
+				"[python]": {
+					"editor.codeActionsOnSave": {
+						"source.organizeImports": true
+					}
+				},
+				"editor.formatOnSave": true,
+				"files.autoSave": "afterDelay",
+				"files.autoSaveDelay": 1000
+			},
+			"extensions": [
+				"ms-python.python",
+				"littlefoxteam.vscode-python-test-adapter",
+				"ms-vsliveshare.vsliveshare",
+				"mhutchie.git-graph",
+				"ms-toolsai.jupyter"
+			]
+		}
+	}
+}

rdock-utils/.gitignore

@@ -0,0 +1,129 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

rdock-utils/Dockerfile

@@ -0,0 +1,10 @@
+FROM python:3.12 AS base
+
+COPY requirements.txt requirements.txt
+RUN python -m pip install --upgrade pip
+RUN python -m pip install -r requirements.txt
+
+FROM base AS development
+
+COPY requirements-dev.txt requirements-dev.txt
+RUN python -m pip install -r requirements-dev.txt

rdock-utils/README.md

@@ -0,0 +1,3 @@
+# rdock-utils python package
+
+coming soon

rdock-utils/pyproject.toml

@@ -0,0 +1,13 @@
+[tool.black]
+line-length = 119
+target-version = ['py312']
+
+[tool.isort]
+profile = "black"
+line_length = 119
+combine_as_imports = true
+
+import_heading_stdlib = "Standard Library"
+import_heading_thirdparty = "Dependencies"
+import_heading_firstparty = "From apps"
+import_heading_localfolder = "Local imports"

rdock-utils/rdock_utils/sdnothing.py

@@ -0,0 +1,2 @@
+def main() -> None:
+    print("to be removed when we start having code migrated over here")

rdock-utils/requirements-dev.txt

@@ -0,0 +1,5 @@
+black
+flake8
+isort
+mypy
+pytest

rdock-utils/scripts/sdnothing

@@ -0,0 +1,12 @@
+#!/usr/bin/env python3
+
+# remove this script when the first script is migrated here
+# actual code for the scripts should be in rdock_utils.<dedicated_script_name_module>
+# for example,
+# from rdock_utils.sdsort import main
+
+# From apps
+from rdock_utils.sdnothing import main
+
+if __name__ == "__main__":
+    main()

rdock-utils/setup.cfg

@@ -0,0 +1,36 @@
+[flake8]
+max-line-length = 119
+exclude = .git,__pycache__
+ignore = E231,E501,E203,W503
+
+
+[mypy]
+python_version = 3.12
+pretty = True
+show_error_context = True
+show_error_codes = True
+
+follow_imports = silent
+ignore_missing_imports = True
+
+disallow_incomplete_defs = True
+disallow_any_generics = True
+disallow_subclassing_any = False
+disallow_untyped_calls = True
+disallow_untyped_defs = True
+disallow_untyped_decorators = True
+
+warn_unused_configs = True
+warn_unreachable = True
+warn_redundant_casts = True
+warn_unused_ignores = True
+warn_return_any = True
+
+check_untyped_defs = True
+
+no_implicit_optional = True
+no_implicit_reexport = False
+
+strict_equality = True
+
+exclude = (^setup\.py$)

rdock-utils/setup.py

@@ -0,0 +1,20 @@
+#!/usr/bin/env python
+
+# Dependencies
+from setuptools import setup
+
+raise Exception("Please make sure you have modified all necessary attributes before pip installing the package")
+
+setup(
+    name="rdock-utils",
+    version="0.01",
+    description="",
+    author="",
+    author_email="",
+    url="",
+    packages=[],
+    # inlcude_package_data=True,
+    # package_data={'package.module':[folder/with/data/*]}
+    # scripts=[],
+    install_requires=[],
+)

rdock-utils/tests/test_all_ok.py

@@ -0,0 +1,6 @@
+# An empty test, to be able to run something with pytest : )
+# Remove me when you have something in place
+
+
+def test_all_ok() -> None:
+    assert True